1. A COMPREHENSIVE GENE REGULATORY NETWORK FOR THE DIAUXIC SHIFT IN SACCHAROMYCES CEREVISIAE GEISTLINGER, L., CSABA, G., DIRMEIER, S., KÜFFNER, R., AND ZIMMER, R. KEVIN MCGEE AND NATALIE WILLIAMS BIOLOGY DEPARTMENT, LOYOLA MARYMOUNT UNIVERSITY JUNE 3, 2015

2. OUTLINE Background: Diauxic shift & comparison of our research with the article Generation of the yeast GRN and the diauxic shift GRN Analysis of the GRN constructed from SGD, YEASTRACT, and Herrgard et al. Summary Implications

3. BACKGROUND Knowledge of which conditions regulation occurs and the effect on expression for a gene were requirements for construction of their GRN. Goal: propose model for large-scale GRNs with a comprehensive model for transcriptional regulation of diauxic shift in yeast Diauxic shift: when yeast cells switch from fermentation to aerobic respiration with the TCA cycle

4. COMPARISON This study wants to distinguish which genes change expression when the cell is under a specific condition Cold shock vs. diauxic shift Construction of GRN Microarray + databases vs. studies and other resources Testing of the GRN ODE to model the dynamics vs. qualitative works to model the dynamics

5. OUTLINE Background: Diauxic shift & comparison of our research with the article Generation of the yeast GRN and the diauxic shift GRN Analysis of the GRN constructed from SGD, YEASTRACT, and Herrgard et al. Summary Implications

6. THE YEAST GRN: FIGURE 1 A combination of direct and indirect evidence provided “high” or “low” confidence in the noted regulations Resources: Saccharomyces Genome Database (SGD) YEASTRACT Herrgard et al.

7. DIAUXIC SHIFT GRN: FIGURE 2 Figure 2 shows the approach used when curating the GRN that controls diauxic shift

8. DIAUXIC SHIFT GRN Petri net models were used to represent the information available in the literature The input of transcriptional transition was defined as a signal or a transcription factor The target gene expression was identified as the output by modeling the fold change in its transcription.

9. DIAUXIC SHIFT GRN: FIGURE 3 Figure 3 is a screenshot of the software RelAnn used to transform literature knowledge to a Petri net transition.

10. OUTLINE Background: Diauxic shift & comparison of our research with the article Generation of the yeast GRN and the diauxic shift GRN Analysis of the GRN constructed from SGD, YEASTRACT, and Herrgard et al. Summary Implications

11. RESULTS: TABLE 1. ANNOTATION SUMMARY Table 1 shows that 322 total interactions involved in the diauxic shift were seen in their GRN. It also categorizes the interactions by the subprocesses involved in this metabolic shift.

12. RESULTS: FIGURE 4 Figure 4 is the Petri net representation of the interactions visualized in flowcharts of the subprocesses of the diauxic shift with CellDesigner.

13. RESULTS: FIGURE 5 Figure 5 is an example of the flowchart of one of the subprocesses of diauxic shift. Regulation Light green: TFs Green & purple ellipses: signals Transcription Yellow: transcription genes Green rhomboids: transcripts Metabolic Light green: translated enzymes Green ellipses: substrates & products Blue hexagons: subprocesses

14. RESULTS: GENERAL COMPARISON SGDYEASTRACTHerrgard et al. Geistlinger et al. 44%N/A29%>96% Improved three aspects of representation of interactions: Context Definition Effect Detailed the regulatory effect type and strength Evidence reliability High – contains both binding and expression evidence (66% interactions had this classification) Low – contains one of the criterion

15. RESULT: FIGURE 6. PCK1 EXAMPLE Figure 6 compares all the information each resource provided as well as what this study achieved in producing through their GRN when analyzing PCK1.

16. OUTLINE Background: Diauxic shift & comparison of our research with the article Generation of the yeast GRN and the diauxic shift GRN Analysis of the GRN constructed from SGD, YEASTRACT, and Herrgard et al. Summary Implications

17. SUMMARY Questions addressed by searching for diauxic shift information: 1.Do existing resources already fully characterize the regulation of a given process? 2.If not, how can such a comprehensive characterization be achieved? 3.Which level of granularity is best suited to represent the volume and detail of the available heterogeneous information?

18. SUMMARY 1.Do existing resources already fully characterize the regulation of a given process? SGD summarizes regulatory impacts such as extra- and intracellular signals YEASTRACT provides binary gene regulatory interactions from binding and expression data Herrgard et al. contains transcriptional data of metabolic genes

19. SUMMARY 2. If not, how can such a comprehensive characterization be achieved? A hierarchical approach was used to: Compile a set of relevant genes Integrate the regulatory information from databases, and Complement the interactions by collecting information from the literature

20. SUMMARY 3. Which level of granularity is best suited to represent the volume and detail of the available heterogeneous information? Representing the regulatory interactions through qualitative characterization (see Figure 4 or 5)

21. OUTLINE Background: Diauxic shift & comparison of our research with the article Generation of the yeast GRN and the diauxic shift GRN Analysis of the GRN constructed from SGD, YEASTRACT, and Herrgard et al. Summary Implications

22. IMPLICATIONS Model can be tested to see if annotated behavior agrees with observed behavior of these regulatory interactions This GRN has 300+ regulations, including combinatorial control, that can: Allow for network-based approaches for interpreting expression data Provide interactive maps and modules integrated into the annotation system Be the starting point to annotate and incorporate other processes

23. REFERENCES Geistlinger, L., Csaba, G., Dirmeier, S., Kϋffner, R., and Zimmer, R. (2013). A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae. Nucleic acids research, 41, 8452-8463.

24. ACKNOWLEDGMENTS Dr. Dahlquist Dr. Fitzpatrick Dondi Fellow researchers and supporters of this dream